Staging Ground Beta 1 Recap, and Reviewers needed for Beta 2. So, supposedly the issue is with Hmisc. More info about Internet Explorer and Microsoft Edge. Learn more about Stack Overflow the company, and our products. Update all/some/none? Already on GitHub? [7] datasets methods base, other attached packages: Working with my work IT department we have now tied this to custom permissions on my workstation that mean that R packages can only be run to pre-specified libraries (in my case "C:\R\R-3.4.3\library"). Loading required package: GenomeInfoDb Thanks for contributing an answer to Stack Overflow! I want to import DESeq2 in Rstudio though and it is giving me a different error when I try importing DESeq2: Error in library("DESeq2") : there is no package called DESeq2. Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support. Is there a proper earth ground point in this switch box? Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications. Whats the grammar of "For those whose stories they are"? Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
library(caret) namespace load failed Object sigma not Sign in Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): Start R to confirm they are gone. Ultimately my colleague helped me to solve the issue by following the steps: Then launching rstudio from within the environment. (Factorization). Also note, however, that the error you got has been associated in the past with mirror outages. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Error: package or namespace load failed for 'DESeq2' packagepackagepackage , RRStudio macOS Mojave 10.14.3 R. I was able to get over this by using g++ for the VORO++ library but I am unsure how this affects the result. After 3-4 manual installs everything worked. Hey, I tried your suggestion and it didn't work as it is but I did figure it out probably with the help of your suggestion. Loading required package: GenomicRanges enter citation("DESeq2")): To install this package, start R (version The error states that the current version is 0.4.5 but 0.4.10 is required. Error: package or namespace load failed for ' tidyverse' in dyn.load (file, DLLpath = DLLpath, . Replacing broken pins/legs on a DIP IC package. Installing DESeq2 Error: no package called GenomeInfoDbData, https://bioconductor.org/packages/3.11/data/annotation/src/contrib/GenomeInfoDbData_1.2.3.tar.gz, https://cran.rstudio.com/bin/macosx/contrib/4.0/RcppArmadillo_0.9.880.1.0.tgz, https://cran.rstudio.com/bin/macosx/contrib/4.0/survival_3.1-12.tgz. Installation path not writeable, unable to update packages: boot, class, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/Hmisc But I guess you have many problems with your installation, and I'd suggest BiocManager::valid () Platform: x86_64-apple-darwin17.0 (64-bit) Checked that the channels are set in the correct order: Asking for help, clarification, or responding to other answers. Connect and share knowledge within a single location that is structured and easy to search. In file.copy(savedcopy, lib, recursive = TRUE) : Installing packages directly into that location fixes the issue but is not desirable for all the reasons that people might want to use custom locations (e.g. a, There are binary versions available but the source versions are later: When you load the package, you can observe this error. [33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3 9543 Abort trap: 6 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}, The downloaded source packages are in Running install.packages("Hmisc") gives the first part of the error with missing cluster.so library. 4. Use of this site constitutes acceptance of our User Agreement and Privacy Making statements based on opinion; back them up with references or personal experience. March 1, 2023, 8:52pm To learn more, see our tips on writing great answers. Find centralized, trusted content and collaborate around the technologies you use most. Old packages: 'RcppArmadillo', 'survival' What is the output of. 1. To learn more, see our tips on writing great answers. Styling contours by colour and by line thickness in QGIS. [9] S4Vectors0.24.4 BiocGenerics0.32.0, loaded via a namespace (and not attached): Error: package or namespace load failed for DESeq2 in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called locfit, Traffic: 307 users visited in the last hour, https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages, User Agreement and Privacy As such there are two solutions that may be more or less attainable given your own IT system. * removing /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/library/DESeq2.
Powered by Discourse, best viewed with JavaScript enabled, DESeq2: Error: package or namespace load failed for DESeq2: objects rowSums, colSums, rowMeans, colMeans are not exported by 'namespace:S4Vectors'. It seems that lots of packages, most importantly data.table and lme4, were not properly compiled. trying URL 'https://wbc.upm.edu.my/cran/bin/windows/contrib/3.6/htmlTable_2.0.1.zip' How can we prove that the supernatural or paranormal doesn't exist? [41] magrittr1.5 RCurl1.98-1.2 tibble3.0.3 Formula1.2-3 cluster2.1.0 im using ubuntu, R ver 4.0.4, bioconductor ver 1.12. That plugin is has not been updated to work with later releases of QIIME 2.
()library(DESeq2):Error in loadNamespace: no package called ""s How do you get out of a corner when plotting yourself into a corner, Identify those arcade games from a 1983 Brazilian music video. Expected in: /Users/nikitavlasenko/miniconda3/envs/renv/lib/R/lib/libR.dylib [45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5 I tried to install Python 3.6 and got 1000s of lines of conflicts, and python version still returns 3.8. when I switch back to my Qiime environment to install Aldex2, I get an error. Warning: restored xfun, The downloaded binary packages are in install.packages("BiocManager"), I get this error: check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Idk, but the issue came up from using installations from within R/Rstudio, and maybe it will never happen if we use just, @NikitaVlasenko you should be able to point Rstudio to the, We've added a "Necessary cookies only" option to the cookie consent popup, DESeqDataSetFromTximport invalid rownames length, deseq2 model design : Different gene output, deseq2 single factor design output interpretation. Platform: x86_64-apple-darwin13.4.0 (64-bit) [46] crayon1.3.4 pkgconfig2.0.3 ellipsis0.3.1 Matrix1.2-18 data.table1.13.0 This includes any installed libraries. Your best bet would be to download the package source code and change the R version and install manually if you wanted the most recent version of locfit to install on your computer. "After the incident", I started to be more careful not to trip over things. If you dont post the error in question (why you cant install Hmisc) no one can help answer your question. Does ZnSO4 + H2 at high pressure reverses to Zn + H2SO4? Why are Suriname, Belize, and Guinea-Bissau classified as "Small Island Developing States"? Error: package or namespace load failed for 'DESeq2': objects 'rowSums', 'colSums', 'rowMeans', 'colMeans' are not exported by 'namespace:S4Vectors' I am using R 3.6.1 and Rstudio 1.2. technocrat August 27, 2020, 10:15pm #2 RedRabbit: DESeq2 requires R 4 and running more than a couple of releases behind in R risks multiplying problems. package in your R session. [7] edgeR_3.16.5 limma_3.30.12 Please remember to confirm an answer once you've received one.
R| - R version 4.0.1 (2020-06-06) locfit version 1.5-9.5 is in the repositories but depends on R (>= 4.1.0) Error in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]) : there is no package called 'data.table' Error: package or namespace load failed for 'DESeq2' Tried installing the missing package: The most common cause of this problem is trying to update a package while it is loaded in R (possibly in another process!). Retrying with flexible solve.Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.Collecting package metadata (repodata.json): doneSolving environment: failed with initial frozen solve. or install using BiocManager that will also install CRAN packages BiocManager::install('locfit'), I couldn't intall locfit but somehow, i did so many different things and it worked. Is the God of a monotheism necessarily omnipotent? Convince your IT department to relax the permissions for R packages Do I need a thermal expansion tank if I already have a pressure tank? My code is GPL licensed, can I issue a license to have my code be distributed in a specific MIT licensed project? to one of the following locations: https://code.bioconductor.org/browse/DESeq2/, https://bioconductor.org/packages/DESeq2/, git clone https://git.bioconductor.org/packages/DESeq2, git clone git@git.bioconductor.org:packages/DESeq2. there is no package called locfit. Making statements based on opinion; back them up with references or personal experience. package rlang was built under R version 3.5.1. If you try loading the DEseq2 library now, that might work. Thanks for contributing an answer to Stack Overflow! How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? there is no package called Hmisc. [6] htmltools0.5.0 base64enc0.1-3 survival3.2-3 rlang0.4.7 pillar1.4.6 I guess that means we can finally close this issue. From the console install.packages ("rlang") should fix this. [21] htmlwidgets1.5.1 latticeExtra0.6-29 knitr1.29 htmlTable2.1.0 Rcpp1.0.5 [1] parallel stats4 stats graphics grDevices utils datasets methods base, other attached packages: [37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8 library ("DESeq2") Error: package or namespace load failed for 'DESeq2' in loadNamespace (j <- i [ [1L]], c (lib.loc, .libPaths ()), versionCheck = vI [ [j]]): there is no package called 'Hmisc' Installing Hmisc as suggested above did not solve the issue. Policy. Acidity of alcohols and basicity of amines.
Error when installing Aldex2 - Community Plugin Support - Open Source now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. When an R package depends on a newer package version, the required package is downloaded but not loaded. Give up and run everything from the "permitted" library location (e.g. Connect and share knowledge within a single location that is structured and easy to search. R version 3.6.1 (2019-07-05) now when I tried installing the missing packages they did install. Bioconductor release. To view documentation for the version of this package installed I tried installing DESeq2 using: but it run into a lot of errors (some missing packages for some dependency packages etc) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
How can I fix error with loading package in R ? | ResearchGate Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05) We've tried this - and can replicate this issue on a completely new install with no existing package installs. Looking for incompatible packages. What I did was - uninstalled everything (R, Rstudio, RTools and deleted the R directory) to eliminate any chance that something was corrupt.
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